To begin, select a square in the population grid to “Set Initial Case.”
You didn't vaccinate an individual. Go back to try again or click the “Skip” button.
Copy the Number of Infectious and Number of Removed values into the “SIR Data Table” in the Current Day column. Or, click the “Autofill” button to automatically enter the numbers for the current day only.
Are you sure you want to clear your progress and start over?
The values you entered in the “SIR Data Table” do not match the Number of Infectious and Number of Removed for the current day.
Are you sure you want to clear all your progress and start over?
Skip to main content
Modeling Disease Spread
 
  • Modeling Disease Spread
  • Welcome
  • Introduction
  • SIR Model Basics
  • SIR Background
  • Tutorial
  • Simulate an Outbreak
  • Summary
  • SIR Model Advanced
  • SIR Background
  • Tutorial
  • Simulate an Outbreak
  • Summary

Welcome to the SIR Model Tutorial!

Let’s explore how we can use this model to simulate the spread of a pathogen in a small population.

Select the button to begin.

1 of 19

Congratulations!

You’ve reached the end of this tutorial! Select “Start Outbreak Simulator” to try a full simulation. Or you can .

19 of 19

Simulation Board

Population Grid

A

B

C

D

E

F

1

2

3

4

5

6

Simulator Status

 

  • Susceptible

    • Susceptible icon
      Susceptible
    • Susceptible and Close Contact icon
      Susceptible
      and Close Contact
    • Susceptible and Close Contact (Highlighted) icon
      Susceptible
      and Close Contact (highlighted)

  • Infectious

    • Newly Infectious icon
      Newly
      Infectious
    • Infectious icon
      Infectious

  • Removed

    • Newly Recovered icon
      Newly
      Recovered
    • Recovered icon
      Recovered
    • Vaccinated icon
      Vaccinated

  • Susceptible

    • Susceptible
    • Susceptible
      and Close Contact
    • Susceptible
      and Close Contact (highlighted)

  • Infectious

    • Newly
      Infectious
    • Infectious

  • Removed

    • Newly
      Recovered
    • Recovered
    • Vaccinated

Settings | Day 0

Before you begin the simulation (Day 0), enter numbers between 1 and 100 as the initial Transmission Probability and initial Recovery Probability.

You can change these two probabilities at the beginning of each day in the simulation.

Transmission and Recovery Probabilities

Transmission Probability (%)
Error: Use a number between 1 and 100
Recovery Probability (%)
Error: Use a number between 1 and 100

Set Initial Case

  • Select an individual in the population grid as the first infectious case in this population.
  • Select the “Set Initial Case” button that appears.
  • To change the initial case, perform the same action on a different individual.

Simulate each day by following these steps:

  1. For each infectious individual in the population grid, select their icon, then “Simulate New Infections.” Select “Done” when finished with all infectious individuals.
  2. Optionally, select one susceptible individual to vaccinate, then select “Done.” Or select “Skip.”
  3. Reveal the number of recovered individuals by selecting “Simulate New Recoveries.”
  4. Copy the numbers of infectious and removed individuals into the “SIR Data Table,” or turn on “Autofill” to automatically fill in the table. Select “End Day” to proceed.
    : off on

    Current Day's Data

    Number of Infectious:
    (Newly infectious + infectious)
    Number of Removed:
    (Newly recovered + recovered + vaccinated)
    Current Day's Data, Infectious: 0
    Current Day's Data, Removed: 0
 

SIR Data Table

SIR Data Table (Table scrolls horizontally)
Day Current Day 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
Susceptible 36
Infectious
Removed

SIR Graph

This graph shows changes in the number of individuals in each group (susceptible, infectious, and removed) over time. Listen to the Graph

Supporting Information

Simulator Help

Supporting Information
HHMI BioInteractive Logo